I'm using NeatDesk, believe it's 4.0.1 or similar version (not near my Mac to confirm the exact version, but it is the latest) and runs on Yosemite. It works well overall, although NeatDesk is prone to crashing intermittently.

I recommend getting into the habit of saving frequently after scans complete, and do not shred the scanned documents until you've verified that what you scanned has successfully saved in the NeatDesk database file.